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Draft Finalreport ECOSYSTEM ASSESSMENT AND NITROGEN MANAGEMENT IN WESTERN BAYS, NEW YORK FINAL REPORT Version 3.0 6Nov14 Prepared for New England Interstate Water Pollution Control Commission Prepared by Thomas Gulbransen1 Larry Swanson2, Katelin Willig2 Mike Owens3, Scott Libby1 Chris Gobler2, Ryan Wallace2 Jeff Cornwell3 Roy Kropp1 Robert Wilson2, Robert J.Diaz4 Rosanna Buhl1 Dongming Yang,2 Cassia Bauer2 Fred Mushacke5 1= Battelle Memorial Institute 2=Stony Brook University, School Of Marine & Atmospheric Science 3=Chesapeake Biogeochemical Associates 4=Diaz & Daughters 5=F.R.E.D. Environmental This report is a work prepared for the United States Government by Battelle. In no event shall either the United States Government or Battelle have any responsibility or liability for any consequences of any use, misuse, inability to use, or reliance on any product, information, designs, or other data contained herein, nor does either warrant or otherwise represent in any way the utility, safety, accuracy, adequacy, efficacy, or applicability of the contents hereof. Ecosystem Assessment and Nitrogen Management in Western Bays, New York Version2.0 CONTENTS 1.0 BACKGROUND OF THIS STUDY ...................................................................................................... 6 2.0 INTRODUCTION TO ISSUES ADDRESSED ..................................................................................... 6 3.0 INTEGRATION OF FINDINGS .......................................................................................................... 10 3.1 Can Evidence of Use Impairments Be Observed Consistently in Areas of the Western Bays? .........................................................................................................10 3.1.1 Shellfishing for Market Purposes ................................................................11 3.1.2 Primary and Secondary Contact Recreation ................................................12 3.1.3 Fishing .........................................................................................................13 3.1.4 Fish Propagation and Survival ....................................................................15 3.1.5 Benthos Status .............................................................................................16 3.2 What are Suitable Indicators/Endpoints of Impairment? .........................................21 3.2.1 Indicator/Endpoint Background ..................................................................21 3.2.2 Regulatory framework for consideration of traditional and alternative endpoints .....................................................................................................25 3.2.3 Physical Representativeness of Western Bays ............................................26 3.2.4 Endpoint evaluation .....................................................................................32 3.3 Are Impairments Linked to Excess Nutrients? ........................................................46 3.3.1 Problematic phytoplankton blooms follow ambient nitrogen .....................46 3.3.2 Algal growth decreases with reductions in dissolved inorganic nitrogen ...47 3.3.3 Nitrogen loads fertilize Ulva growth & hazardous deposition ....................49 3.3.4 Role of nitrogen in fish propagation ............................................................53 3.3.5 Impairments without quantitative linkage to nitrogen ................................53 3.4 Which Nitrogen Management Practices Are Most Promising? ...............................57 3.4.1 Nitrogen loads into Western Bays ecosystem .............................................58 3.4.2 Nitrogen loads into Western Bays waterbody .............................................63 3.4.3 Nitrogen management plan (NMP) options ................................................68 3.4.4 Western Bays nitrogen management plan options decision model .............71 3.4.5 Commentary on select nitrogen management plan options.........................75 4.0 REFERENCES ..................................................................................................................................... 79 APPENDICES Appendix A: Nutrient Assessment and Management in Shallow Coastal Waters of Hempstead Bay Appendix B: Benthic Infauna Appendix C: Hempstead Bay Water Quality Studies: Sediment Profile Imaging Appendix D: A Synthesis of Loadings, Monitoring Information, and Impairments in the Western Bays Appendix E: Quantitative Description of the Spatial Patterns in Residence Times within the Hempstead Bays Region appendix F: Historical Water Quality Monitoring Data for Western Bays as Measured by Town of Hempstead Appendix G: Hempstead Bay Sediment Nutrient Fluxes –Final Report Appendix H: Regarding Tidal Wetland Trends in Western Hempstead Bay Appendix I: Response to Comments 2013 Appendix J: Response to Comments 2014 November 6, 2014 FINAL Page 2 of 93 Ecosystem Assessment and Nitrogen Management in Western Bays, New York Version2.0 LIST OF FIGURES Figure 1. General extent of the Western Bays shallow embayments study area along with associated watershed and sewershed of ~500,000 people (2010 Census). ......................... 6 Figure 2. Draft Conceptual Model of nitrogen cycling through Western Bays’ canals, channels, mudflats and inlets .............................................................................................. 8 Figure 3. NYS DEC Waterbody use designations for segments of Western Bays. .................................... 10 Figure 4. Harmful dinoflagellates Alexandrium fundyense and Dinophysis acuminata found in Hewlett Bay and Middle Bay 2010. .................................................................................. 12 Figure 5. Average Dissolved Oxygen levels at the surface in Reynolds Channel during summers 2003-2009. (The solid line is the average of all measurements). ...................... 13 Figure 6. Dissolved Oxygen data from Bay Park outfall, Hog Island, Middle Bay, East Bay and Jones Inlet, as sampled by SoMAS 2012 relative to acute standard of never less than 3.0mg/L. ................................................................................................... 14 Figure 7. Dissolved Oxygen data from Hewlett Bay, as sampled by SoMAS 2011. .................................. 14 Figure 8. Vertical cross section profile of dissolved oxygen concentrations (mg/ L) with salinity (ppt) contour lines in Hewlett Bay during early September of 2012. .................. 15 Figure 9. Vertical cross section profile of pH (total scale) with salinity (ppt) contour lines in Hewlett Bay during early September of 2012. .................................................................. 16 Figure 10. Number of benthic species observed in Fall 2012. .................................................................... 17 Figure 11. Non-metric Multi-dimensional Scaling plot of Bray-Curtis similarity. Outlier 1 and Outlier 2 are the least similar of the “groups”. ................................................................. 18 Figure 12. Number of macrobenthic species observed in Western Bays stations Fall 2012. ..................... 19 Figure 13. The percent of sediment classified as fine grained at each Western Bays station Fall 2012 (%; 100-(sand+gravel)). .................................................................................... 19 Figure 14. Hempstead Bay SPI images; core photos; quartiles of water quality, Ulva % cover, % fines; and infaunal similarity group #. Composite figures for Middle Bay and East Bay are available in Appendix C. ....................................................................... 20 Figure 15. Example of multilevel endpoints associated with eutrophication (Bricker et al. 2003) ................................................................................................................................. 24 Figure 16. Excerpt from NYS DEC 2009b consolidated assessment and listing methodology. ................ 26 Figure 17. U.S. Coast and Geodetic Survey 1879-1880 topographic map (left) and 1897 Hyde and company map (right) showing shallow TIDAL wetlands of the Western Bays and coastal inlets. ..................................................................................................... 28 Figure 18. High resolution bathymetry (m) interpolated to refined model grid. ........................................ 29 Figure 19. Surface salinity (PSU 29.5-32) measured in Western Bays September 2012. .......................... 30 Figure 20. Tidally averaged bottom salinity (PSU) modeled within Hempstead Bay and Middle Bay. ...................................................................................................................... 30 Figure 21. Residence time (hours) distribution in Hempstead Bay and Middle Bay. ................................. 31 Figure 22. Nitrate concentrations (µM) for USGS mooring, SoMAS Hewlett Bay average, ELAP HB stations, and ELAP station ToH3 near mooring. ............................................. 37 Figure 23. Dissolved ammonium concentrations (µM) across Western Bays from during late September 2012. ............................................................................................................... 38 Figure 24. Total Organic Carbon (percent) as reported by SoMAS (Brownawell 2013) ........................... 43 Figure 25. Chlorophyll a (upper left, ug/L); Dissolved Nitrate (upper right, uM); Dissolved Ammonium (lower left, uM);Dissolved Nitrate (lower right, uM) in Western Bays summer 2012. ..........................................................................................................
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